How could the civil war be considered a coup d'etat?

One figure you might want to read up on is Aaron Burr. He was Vice President under Jefferson, and was eventually charged with treason. He was accused of plotting with a cabal of other powerful figures to seize territory on the frontier and create an independent state there. He was acquitted for lack of evidence though, and the exact details of his conspiracy are hazy, because, well, it was a conspiracy, and he denied any part in it, so it had to be pieced together, and the result was not convincing enough to see him convicted.

He fled the country after the trial and spent a long time in exile. Interestingly enough, this is also the guy who shot Alexander Hamilton in a duel. One of US history's most fascinating 'villains.'

The closest the United States ever came to a coup was likely the Newburgh Conspiracy of 1783, though historians generally conclude that there wasn't any real desire to overthrow the government, but rather an attempt to use the fear of the Continental Army overthrowing the government to attain a political goal.

After Yorktown, the British stopped actively campaigning in North America, focusing on retaining their colonial possessions in the Caribbean and India, and began negotiating the end of the war. Washington and the Continental Army encamped at Newburgh, NY, north of New York City, to monitor the British Army and be prepared to occupy the city when and if the British withdrew, while waiting word of a final peace settlement.

The current government of the United States was under the Articles of Confederation, which was something of a toothless government without the authority to levy taxes, and thus the inability to pay the pensions the Continental soldiers had been promised. As the war drew to a close, everyone understood that the dissolution of the army would remove their leverage to ensure that they received their pensions. Members of Congress trying to apply pressure to Congress and the States to guarantee the pensions communicated with officers of the Continental Army trying to determine how best to use the army's leverage to get that guarantee.

At this point, the Continental Army was in much the same position as the New Model Army was at the end of the Second English Civil War. The war was won, the final settlement was being negotiated, and the army was about be dissolved without any guarantee of being paid for having won the war. The New Model Army had decided to overthrow Parliament, purging it of members not on board with putting Charles I on trial for treason, and ultimately setting Oliver Cromwell up as king in all but name.

In March, an anonymous letter circulated around the camp in Newburgh calling for a meeting on March 11th of the field officers to discuss sending Congress and ultimatum. When Washington saw the letter, he sent out orders objecting to the meeting having been called for in such a manner, and instead called for a meeting to be held on the 15th, with a report of the meeting to be sent to him by the senior officer present (implying that he would not be attending).

When the meeting began, Washington surprised the officers by attending the meeting himself, and giving an impassioned speech begging the army to not "open the floodgates of civil discord and deluge our rising empire in blood." He then said he had received a letter from Congress, and took it out to read to the assembly. He stared at the paper for some time, then reached into his pocket and pulled out a pair of spectacles, which most of the men in the room had never seen him wear. He then said, "Gentlemen, you will permit me to put on my spectacles, for I have not only grown gray but almost blind in the service of my country."

This essentially ended the conspiracy, as Washington shamed the officers for even contemplating the threat of a coup. Now, as I said, there probably wasn't a plan to really overthrow the government, but Washington knew that it was important to at the outset establish that republican government couldn't exist if that was contemplated as even a possibility.

Ultimately, Congress approved a five year pension, the army was disbanded after the signing of the Treaty of Paris, and Washington resigned his commission, intending to retire to private life for good (history had other plans for him).

In 1862, the government of the United States feared that George McClellan would attempt to overthrow the government when he was removed from command of the Army of the Potomac - he was a charismatic leader who was practically worshiped by his men, and most of the officers of the army were personally loyal to him, but for all his flaws as a general and a man, McClellan had no desire to repeat Napoleon's 18 Brumaire, and returned home after his sacking, only attempting to remove the ruling government through democratic means in 1864, where he was the Democratic Party nominee for President.

Here's an old post by /u/infamousbrad about one example people talk about as a possible attempted coup (but, as the top answer indicates, probably not a real, serious one), the "business plot": https://www.reddit.com/r/AskHistorians/comments/2i80bz/the_business_plot_conspiracy_in_1933_gen_smedley/?st=iytsahfk&sh=ea1c2b8e

Wasn't there concerns during Nixon's impeachment that he could get the US Marine Corps based in Washington DC to prevent him from being hauled out of the White House?

Follow up question: of the hasn't been, why not? Haven't large amounts of the population been unhappy with the government before?